gatk3的最后一个经典版本3.8

Guillermo del Angel 2ab270cf3f Corner case fix to General Ploidy SNP likelihood model. ... -- In case there are no informative bases in a pileup but pileup isn't empty (like when all bases have Q < min base quality) the GLs were still computed (but were all zeros) and fed to the exact model. Now, mimic case of diploid Gl computation where GLs are only added if # good bases > 0 -- I believe general case where only non-informative GLs are fed into AF calc model is broken and yields bogus QUAL, will investigate separately.		2013-04-23 21:13:18 -04:00
licensing	Removing the symlink from the private license file	2013-02-09 12:57:44 -05:00
protected	Corner case fix to General Ploidy SNP likelihood model.	2013-04-23 21:13:18 -04:00
public	Minor: bump up the amount of cached log10 data in MathUtils so that Monkol can actually call 50K samples.	2013-04-19 08:39:08 -04:00
settings	Don't allow users to specify keys and IDs that contain angle brackets or equals signs (not allowed in VCF spec).	2013-04-05 00:52:32 -04:00
.gitignore	Fixing the licensing scripts	2013-01-26 13:42:49 -05:00
build.xml	Add additional necessary class files to na12878kb.jar target	2013-04-23 14:03:48 -04:00
intellij_example.tar.bz2	Removed the intellij files from the root and made an example package for new users. This allows users to start at the same page and then change it as they see fit without interfering with the repo (thanks guillermo!)	2012-09-27 11:04:56 -04:00
ivy.xml	Brought all of ReduceReads to fastutils	2013-02-23 22:53:23 -05:00